Setup

FastQC Summary

Summary statistics for all libraries
Filename Total Flagged As Poor Quality Sequence Length %GC
2.Illumina_indexing-35.CP-4937_R1.fastq.gz 168,489,110 0 50-151 42
2.Illumina_indexing-35.CP-4937_R2.fastq.gz 168,489,110 0 50-151 42
2.Illumina_indexing-5.CP-4935_R1.fastq.gz 169,465,652 0 50-151 42
2.Illumina_indexing-5.CP-4935_R2.fastq.gz 169,465,652 0 50-151 42
2.Illumina_indexing-6.CP-4936_R1.fastq.gz 176,714,410 0 50-151 42
2.Illumina_indexing-6.CP-4936_R2.fastq.gz 176,714,410 0 50-151 42

Read Totals

Library Sizes ranged between 168,489,110 and 176,714,410 reads.

Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.

FastQC Summary

Summary of FastQC flags for each parameter

Per Base Sequence Quality

Heatmap showing mean base qualities for each library

Per Sequence Quality Scores

Heatmap showing mean sequence qualities for each library

Per Base Sequence Content

Heatmap of summed base distributions along each read

Per Sequence GC Content

GC Content Heatmap normalised to theoretical GC content in the Btaurus Genome

GC Content Distributions for all reads showing theoretical GC content from the Btaurus Genome

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented Sequences

Adapter Content

Universal Adapter Content

Kmer Content

Summary of Overrepresented Kmers in all files. A maximum of 30 Kmers are shown.
Filename Sequence Count PValue Obs/Exp_Max Max_Obs/Exp_Position
2.Illumina_indexing-6.CP-4936_R1 GATCAAT 298,000 0 7.37 1
2.Illumina_indexing-35.CP-4937_R1 GATCAAT 283,070 0 7.253 1
2.Illumina_indexing-5.CP-4935_R1 GATCAAT 282,530 0 6.919 1
2.Illumina_indexing-6.CP-4936_R1 GATCACA 595,825 0 7.149 1
2.Illumina_indexing-5.CP-4935_R1 GATCACA 577,970 0 7.336 1
2.Illumina_indexing-35.CP-4937_R1 GATCACA 568,850 0 7.164 1
2.Illumina_indexing-6.CP-4936_R2 GATCACA 478,705 0 8.09 1
2.Illumina_indexing-5.CP-4935_R2 GATCACA 464,595 0 8.446 1
2.Illumina_indexing-35.CP-4937_R2 GATCACA 458,220 0 8.131 1
2.Illumina_indexing-6.CP-4936_R1 GATCACT 296,385 0 7.046 1
2.Illumina_indexing-5.CP-4935_R1 GATCACT 289,550 0 7.311 1
2.Illumina_indexing-35.CP-4937_R1 GATCACT 282,860 0 6.987 1
2.Illumina_indexing-6.CP-4936_R1 GATCATC 326,640 0 6.227 1
2.Illumina_indexing-5.CP-4935_R1 GATCATC 314,470 0 6.094 1
2.Illumina_indexing-35.CP-4937_R1 GATCATC 308,310 0 6.466 1
2.Illumina_indexing-6.CP-4936_R2 GATCATC 285,125 0 6.401 1
2.Illumina_indexing-5.CP-4935_R2 GATCATC 277,335 0 6.387 1
2.Illumina_indexing-6.CP-4936_R1 GATCATG 445,890 0 6.672 1
2.Illumina_indexing-5.CP-4935_R1 GATCATG 424,670 0 6.331 1
2.Illumina_indexing-35.CP-4937_R1 GATCATG 423,785 0 6.324 1
2.Illumina_indexing-6.CP-4936_R2 GATCATG 396,330 0 6.666 1
2.Illumina_indexing-5.CP-4935_R2 GATCATG 377,060 0 6.573 1
2.Illumina_indexing-35.CP-4937_R2 GATCATG 373,905 0 6.583 1
2.Illumina_indexing-6.CP-4936_R2 GATCATT 370,370 0 6.383 1
2.Illumina_indexing-5.CP-4935_R2 GATCATT 355,985 0 6.356 1
2.Illumina_indexing-6.CP-4936_R1 GATCCAA 284,805 0 6.314 1
2.Illumina_indexing-5.CP-4935_R1 GATCCAA 274,560 0 6.413 1
2.Illumina_indexing-6.CP-4936_R1 GATCCCT 313,990 0 6.365 1
2.Illumina_indexing-5.CP-4935_R1 GATCCCT 303,765 0 6.33 1
2.Illumina_indexing-35.CP-4937_R2 GATCCCT 292,290 0 6.219 1